Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9707243.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9707243.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9707243.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.86, per 1000 atoms: 0.28 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.726 distance_ideal: 2.720 ideal - model: -0.006 slack: 0.000 delta_slack: -0.006 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.725 distance_ideal: 2.710 ideal - model: -0.015 slack: 0.000 delta_slack: -0.015 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 117.9 milliseconds Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.05: 1103 1.05 - 1.30: 2445 1.30 - 1.54: 1741 1.54 - 1.79: 637 1.79 - 2.03: 8 Bond restraints: 5934 Sorted by residual: bond pdb=" CG GLU B 66 " pdb=" HG3 GLU B 66 " ideal model delta sigma weight residual 0.970 1.394 -0.424 2.00e-02 2.50e+03 4.50e+02 bond pdb=" CA VAL B 62 " pdb=" C VAL B 62 " ideal model delta sigma weight residual 1.520 1.719 -0.199 1.00e-02 1.00e+04 3.97e+02 bond pdb=" NH1 ARG A 143 " pdb="HH12 ARG A 143 " ideal model delta sigma weight residual 0.860 1.252 -0.392 2.00e-02 2.50e+03 3.83e+02 bond pdb=" CA ILE A 162 " pdb=" C ILE A 162 " ideal model delta sigma weight residual 1.524 1.291 0.233 1.22e-02 6.72e+03 3.65e+02 bond pdb=" N ARG B 175 " pdb=" CA ARG B 175 " ideal model delta sigma weight residual 1.459 1.240 0.219 1.20e-02 6.94e+03 3.33e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 5491 3.98 - 7.96: 3462 7.96 - 11.94: 1497 11.94 - 15.92: 326 15.92 - 19.90: 34 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.37 109.69 12.68 7.30e-01 1.88e+00 3.02e+02 angle pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " pdb=" NH2 ARG A 83 " ideal model delta sigma weight residual 119.20 134.69 -15.49 9.00e-01 1.23e+00 2.96e+02 angle pdb=" O VAL B 112 " pdb=" C VAL B 112 " pdb=" N LEU B 113 " ideal model delta sigma weight residual 121.98 134.59 -12.61 8.90e-01 1.26e+00 2.01e+02 angle pdb=" O GLY A 174 " pdb=" C GLY A 174 " pdb=" N ARG A 175 " ideal model delta sigma weight residual 123.48 137.21 -13.73 1.00e+00 1.00e+00 1.88e+02 angle pdb=" O ALA A 104 " pdb=" C ALA A 104 " pdb=" N ILE A 105 " ideal model delta sigma weight residual 123.44 139.65 -16.21 1.23e+00 6.61e-01 1.74e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.74: 1864 17.74 - 35.47: 125 35.47 - 53.19: 40 53.19 - 70.92: 17 70.92 - 88.64: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.238: 203 0.238 - 0.475: 173 0.475 - 0.713: 82 0.713 - 0.950: 30 0.950 - 1.187: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA TYR B 195 " pdb=" N TYR B 195 " pdb=" C TYR B 195 " pdb=" CB TYR B 195 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.52e+01 chirality pdb=" CA THR B 20 " pdb=" N THR B 20 " pdb=" C THR B 20 " pdb=" CB THR B 20 " both_signs ideal model delta sigma weight residual False 2.53 3.55 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CA ILE B 70 " pdb=" N ILE B 70 " pdb=" C ILE B 70 " pdb=" CB ILE B 70 " both_signs ideal model delta sigma weight residual False 2.43 1.41 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.137 2.00e-02 2.50e+03 7.63e-02 1.74e+02 pdb=" CG PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.070 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.027 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.020 2.00e-02 2.50e+03 7.28e-02 1.59e+02 pdb=" CG PHE A 119 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.110 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.088 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.090 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.135 2.00e-02 2.50e+03 6.62e-02 1.31e+02 pdb=" CG TYR A 194 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.058 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.046 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.056 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.117 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " -0.050 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.53: 19 1.53 - 2.30: 1715 2.30 - 3.07: 21504 3.07 - 3.83: 33265 3.83 - 4.60: 53792 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110295 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.763 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.002 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.030 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.148 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.180 2.620 ... (remaining 110290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 12 15.96 2 Mg 2 11.97 3 O 1357 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2984 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6693 n_use_u_iso = 3419 n_use_u_aniso = 3274 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 6693 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6693 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3419 aniso = 3274) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1426 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_9707243_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2040 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.303940 | | target function (ml) not normalized (work): 806183.849812 | | target function (ml) not normalized (free): 16550.869600 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2133 0.2026 6.6717 6.3212| | 2: 2.94 - 2.33 1.00 7339 128 0.1615 0.1659 5.5567 5.6032| | 3: 2.33 - 2.04 0.96 6939 150 0.1631 0.1674 5.1622 5.2173| | 4: 2.04 - 1.85 1.00 7170 155 0.1789 0.1683 4.9765 5.1138| | 5: 1.85 - 1.72 0.99 7113 159 0.1932 0.1864 4.7984 4.8114| | 6: 1.72 - 1.62 0.99 7102 142 0.1977 0.1847 4.6649 4.6548| | 7: 1.62 - 1.54 0.99 7104 148 0.2029 0.1624 4.5625 4.5138| | 8: 1.54 - 1.47 0.96 6798 152 0.2055 0.2202 4.4836 4.5502| | 9: 1.47 - 1.41 0.98 6938 155 0.2078 0.1968 4.3873 4.3928| | 10: 1.41 - 1.36 0.99 7022 150 0.2123 0.1983 4.3096 4.2673| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2016 4.2322 4.1998| | 12: 1.32 - 1.28 0.98 6976 149 0.2079 0.1985 4.1686 4.2314| | 13: 1.28 - 1.25 0.98 6907 166 0.2038 0.2113 4.1328 4.166| | 14: 1.25 - 1.22 0.98 7015 113 0.2109 0.2188 4.0884 4.1686| | 15: 1.22 - 1.19 0.98 6957 137 0.2111 0.1918 4.0448 3.9772| | 16: 1.19 - 1.17 0.93 6604 132 0.2154 0.2380 4.0123 4.1354| | 17: 1.17 - 1.14 0.98 6941 135 0.2190 0.1984 3.9702 4.0205| | 18: 1.14 - 1.12 0.98 6875 142 0.2221 0.2274 3.9257 3.9065| | 19: 1.12 - 1.10 0.97 6949 106 0.2260 0.2383 3.8714 3.9757| | 20: 1.10 - 1.08 0.97 6884 147 0.2312 0.2515 3.8266 3.9559| | 21: 1.08 - 1.07 0.97 6852 152 0.2469 0.2656 3.7987 3.8112| | 22: 1.07 - 1.05 0.97 6838 135 0.2612 0.2513 3.7681 3.7492| | 23: 1.05 - 1.03 0.97 6829 159 0.2705 0.2663 3.7285 3.8542| | 24: 1.03 - 1.02 0.96 6785 133 0.2916 0.2787 3.7072 3.7488| | 25: 1.02 - 1.01 0.93 6552 130 0.3099 0.2893 3.6763 3.7121| | 26: 1.01 - 0.99 0.96 6767 158 0.3223 0.3544 3.624 3.6623| | 27: 0.99 - 0.98 0.94 6648 131 0.3413 0.3158 3.6447 3.607| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.83 0.91 0.97 36815.00| | 2: 2.94 - 2.33 7339 128 0.85 21.91 1.08 1.01 15934.59| | 3: 2.33 - 2.04 6939 150 0.92 13.45 1.11 1.04 4617.50| | 4: 2.04 - 1.85 7170 155 0.92 14.29 1.12 1.06 3014.42| | 5: 1.85 - 1.72 7113 159 0.91 15.83 1.12 1.08 2137.13| | 6: 1.72 - 1.62 7102 142 0.90 16.53 1.11 1.08 1603.54| | 7: 1.62 - 1.54 7104 148 0.90 16.98 1.11 1.07 1243.75| | 8: 1.54 - 1.47 6798 152 0.90 17.34 1.10 1.06 1040.46| | 9: 1.47 - 1.41 6938 155 0.89 17.72 1.10 1.06 862.41| | 10: 1.41 - 1.36 7022 150 0.88 18.64 1.09 1.06 746.81| | 11: 1.36 - 1.32 6997 151 0.88 18.66 1.08 1.05 651.02| | 12: 1.32 - 1.28 6976 149 0.88 18.96 1.08 1.05 602.09| | 13: 1.28 - 1.25 6907 166 0.88 18.95 1.07 1.06 571.90| | 14: 1.25 - 1.22 7015 113 0.87 20.06 1.08 1.05 550.32| | 15: 1.22 - 1.19 6957 137 0.87 20.03 1.08 1.05 513.47| | 16: 1.19 - 1.17 6604 132 0.87 20.44 1.08 1.03 482.60| | 17: 1.17 - 1.14 6941 135 0.86 21.19 1.08 1.01 446.61| | 18: 1.14 - 1.12 6875 142 0.86 21.98 1.08 0.98 422.33| | 19: 1.12 - 1.10 6949 106 0.84 23.16 1.08 0.99 408.10| | 20: 1.10 - 1.08 6884 147 0.84 23.84 1.06 0.97 378.36| | 21: 1.08 - 1.07 6852 152 0.83 24.95 1.06 0.97 355.78| | 22: 1.07 - 1.05 6838 135 0.82 25.93 1.06 0.96 330.12| | 23: 1.05 - 1.03 6829 159 0.80 27.63 1.06 0.97 329.08| | 24: 1.03 - 1.02 6785 133 0.78 29.36 1.05 0.96 323.21| | 25: 1.02 - 1.01 6552 130 0.76 31.01 1.03 0.91 310.65| | 26: 1.01 - 0.99 6767 158 0.74 32.66 1.03 0.90 290.60| | 27: 0.99 - 0.98 6648 131 0.76 31.83 1.03 0.90 266.41| |alpha: min = 0.90 max = 1.08 mean = 1.01| |beta: min = 266.41 max = 36815.00 mean = 2919.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.55| |phase err.(test): min = 0.00 max = 89.05 mean = 21.38| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.265 2950 Z= 5.496 Angle : 5.170 16.757 4018 Z= 3.685 Chirality : 0.394 1.187 492 Planarity : 0.034 0.147 512 Dihedral : 12.695 88.645 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.11 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 5.48 % Favored : 93.87 % Cbeta Deviations : 37.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.36), residues: 386 helix: -2.83 (0.28), residues: 144 sheet: -1.27 (0.50), residues: 86 loop : -0.54 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.023 ARG B 149 TYR 0.098 0.035 TYR A 192 PHE 0.097 0.033 PHE A 119 TRP 0.104 0.031 TRP A 146 HIS 0.069 0.029 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2040 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.303940 | | target function (ml) not normalized (work): 806183.849812 | | target function (ml) not normalized (free): 16550.869600 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2038 0.2040 0.1997 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2038 0.2040 0.1997 n_refl.: 191155 remove outliers: r(all,work,free)=0.2039 0.2040 0.1997 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2038 0.2040 0.1997 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1942 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1804 0.1942 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4240 400.535 294.055 0.431 0.918 0.301 13.296-10.522 100.00 100 1 0.2523 534.497 521.084 0.784 0.920 0.253 10.503-8.327 99.45 178 3 0.2557 565.118 556.172 0.971 0.920 0.230 8.318-6.595 100.00 360 8 0.2445 414.736 403.072 0.969 0.919 0.175 6.588-5.215 100.00 711 7 0.2236 381.101 365.943 0.954 0.919 0.170 5.214-4.128 98.38 1367 28 0.1496 557.435 549.739 1.072 0.919 0.090 4.126-3.266 94.74 2603 46 0.1335 508.132 498.767 1.138 0.920 0.019 3.266-2.585 99.86 5447 97 0.1449 342.774 338.020 1.111 0.919 0.010 2.585-2.046 97.45 10613 204 0.1393 258.603 254.489 1.118 0.918 0.000 2.046-1.619 99.39 21536 464 0.1620 153.054 149.874 1.141 0.916 0.000 1.619-1.281 98.00 42464 925 0.1926 82.395 80.164 1.122 0.914 0.000 1.281-0.980 96.53 101826 2056 0.2336 44.203 41.668 1.110 0.909 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0087 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1942 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1806 r_free=0.1943 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.618628 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.208374 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1507 0.0235 0.039 1.2 10.5 0.0 0.3 0 11.309 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.07 2.35 1.117 13.108 576.208 0.019 13.01 15.76 2.75 1.255 13.345 576.208 0.018 Individual atomic B min max mean iso aniso Overall: 5.28 73.04 15.03 1.41 435 3274 Protein: 5.28 40.31 11.01 1.41 0 2902 Water: 6.31 73.04 29.49 N/A 435 370 Other: 15.98 30.16 23.07 N/A 0 2 Chain A: 5.35 59.64 13.06 N/A 0 1626 Chain B: 5.28 73.04 12.78 N/A 0 1648 Chain S: 11.73 62.65 30.88 N/A 435 0 Histogram: Values Number of atoms 5.28 - 12.06 2181 12.06 - 18.83 632 18.83 - 25.61 311 25.61 - 32.38 261 32.38 - 39.16 154 39.16 - 45.94 110 45.94 - 52.71 37 52.71 - 59.49 16 59.49 - 66.26 6 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1576 r_work=0.1300 r_free=0.1572 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1572 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1286 r_free = 0.1562 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1286 r_free= 0.1562 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015687 | | target function (ls_wunit_k1) not normalized (work): 2938.230823 | | target function (ls_wunit_k1) not normalized (free): 117.602237 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1286 0.1562 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1475 0.1473 0.1638 n_refl.: 191141 remove outliers: r(all,work,free)=0.1475 0.1473 0.1638 n_refl.: 191141 overall B=0.17 to atoms: r(all,work,free)=0.1500 0.1497 0.1648 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1277 0.1551 n_refl.: 191141 remove outliers: r(all,work,free)=0.1282 0.1277 0.1550 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3587 402.814 371.360 0.483 0.962 0.285 13.296-10.522 100.00 100 1 0.2085 534.497 527.118 0.744 0.964 0.240 10.503-8.327 99.45 178 3 0.1762 565.118 562.828 0.890 0.964 0.217 8.318-6.595 100.00 360 8 0.1701 414.736 411.859 0.912 0.963 0.160 6.588-5.215 100.00 711 7 0.1526 381.101 373.845 0.889 0.964 0.160 5.214-4.128 98.38 1367 28 0.0898 557.435 554.376 0.979 0.964 0.080 4.126-3.266 94.74 2603 46 0.0832 508.132 504.375 1.044 0.964 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.398 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 256.386 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.387 1.057 0.964 0.000 1.619-1.281 98.00 42464 925 0.1283 82.395 81.399 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.154 1.026 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0386 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1550 | n_water=805 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1282 r_free=0.1554 | n_water=794 | time (s): 99.560 (total time: 102.620) Filter (q & B) r_work=0.1282 r_free=0.1555 | n_water=789 | time (s): 4.410 (total time: 107.030) Compute maps r_work=0.1282 r_free=0.1555 | n_water=789 | time (s): 2.400 (total time: 109.430) Filter (map) r_work=0.1308 r_free=0.1524 | n_water=648 | time (s): 4.910 (total time: 114.340) Find peaks r_work=0.1308 r_free=0.1524 | n_water=648 | time (s): 0.890 (total time: 115.230) Add new water r_work=0.1332 r_free=0.1557 | n_water=955 | time (s): 5.200 (total time: 120.430) Refine new water occ: r_work=0.1289 r_free=0.1510 adp: r_work=0.1276 r_free=0.1511 occ: r_work=0.1278 r_free=0.1508 adp: r_work=0.1272 r_free=0.1509 occ: r_work=0.1273 r_free=0.1507 adp: r_work=0.1271 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1508 r_work=0.1271 r_free=0.1508 | n_water=955 | time (s): 76.270 (total time: 196.700) Filter (q & B) r_work=0.1274 r_free=0.1513 | n_water=885 | time (s): 5.270 (total time: 201.970) Filter (dist only) r_work=0.1275 r_free=0.1513 | n_water=884 | time (s): 108.950 (total time: 310.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.825990 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 579.719045 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1260 0.1532 0.0272 0.042 1.1 20.4 0.0 0.3 0 11.413 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.60 15.32 2.72 2.047 15.182 579.719 0.015 12.39 15.21 2.82 2.425 15.223 579.719 0.014 Individual atomic B min max mean iso aniso Overall: 5.35 68.46 16.29 1.19 516 3272 Protein: 5.35 39.73 10.99 1.19 0 2902 Water: 6.60 68.46 33.67 N/A 516 368 Other: 16.32 32.77 24.54 N/A 0 2 Chain A: 5.56 56.24 13.00 N/A 0 1624 Chain B: 5.35 68.46 12.82 N/A 0 1648 Chain S: 11.80 66.90 37.74 N/A 516 0 Histogram: Values Number of atoms 5.35 - 11.66 2057 11.66 - 17.97 713 17.97 - 24.28 260 24.28 - 30.59 214 30.59 - 36.90 183 36.90 - 43.22 171 43.22 - 49.53 93 49.53 - 55.84 49 55.84 - 62.15 38 62.15 - 68.46 10 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1520 r_work=0.1239 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1522 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1517 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013633 | | target function (ls_wunit_k1) not normalized (work): 2553.480728 | | target function (ls_wunit_k1) not normalized (free): 103.203728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1232 0.1517 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1445 0.1442 0.1603 n_refl.: 191139 remove outliers: r(all,work,free)=0.1445 0.1442 0.1603 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1442 0.1439 0.1602 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1238 0.1523 n_refl.: 191139 remove outliers: r(all,work,free)=0.1244 0.1238 0.1523 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3287 402.814 377.459 0.489 0.962 0.267 13.296-10.522 100.00 100 1 0.1884 534.497 527.266 0.767 0.963 0.223 10.503-8.327 99.45 178 3 0.1434 565.118 567.411 0.921 0.963 0.188 8.318-6.595 100.00 360 8 0.1598 414.736 412.464 0.941 0.962 0.177 6.588-5.215 100.00 711 7 0.1347 381.101 376.832 0.913 0.962 0.147 5.214-4.128 98.38 1367 28 0.0835 557.435 556.141 0.996 0.962 0.110 4.126-3.266 94.74 2603 46 0.0773 508.132 505.364 1.060 0.962 0.016 3.266-2.585 99.86 5447 97 0.0858 342.774 341.253 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.751 1.059 0.960 0.000 2.046-1.619 99.39 21536 464 0.1050 153.054 151.601 1.081 0.958 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.347 1.074 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.214 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0490 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1238 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1238 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1238 r_free=0.1523 | n_water=884 | time (s): 3.550 (total time: 3.550) Filter (dist) r_work=0.1240 r_free=0.1520 | n_water=880 | time (s): 110.210 (total time: 113.760) Filter (q & B) r_work=0.1240 r_free=0.1519 | n_water=876 | time (s): 4.970 (total time: 118.730) Compute maps r_work=0.1240 r_free=0.1519 | n_water=876 | time (s): 2.210 (total time: 120.940) Filter (map) r_work=0.1278 r_free=0.1527 | n_water=690 | time (s): 4.580 (total time: 125.520) Find peaks r_work=0.1278 r_free=0.1527 | n_water=690 | time (s): 0.840 (total time: 126.360) Add new water r_work=0.1304 r_free=0.1570 | n_water=1002 | time (s): 4.760 (total time: 131.120) Refine new water occ: r_work=0.1258 r_free=0.1518 adp: r_work=0.1259 r_free=0.1519 occ: r_work=0.1254 r_free=0.1513 adp: r_work=0.1254 r_free=0.1515 occ: r_work=0.1252 r_free=0.1509 adp: r_work=0.1251 r_free=0.1511 ADP+occupancy (water only), MIN, final r_work=0.1251 r_free=0.1511 r_work=0.1251 r_free=0.1511 | n_water=1002 | time (s): 330.300 (total time: 461.420) Filter (q & B) r_work=0.1255 r_free=0.1519 | n_water=872 | time (s): 4.780 (total time: 466.200) Filter (dist only) r_work=0.1255 r_free=0.1519 | n_water=870 | time (s): 115.650 (total time: 581.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.714602 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.214332 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1243 0.1444 0.0201 0.035 1.1 7.1 0.0 0.0 0 0.857 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.43 14.44 2.01 1.930 14.574 17.214 3.943 12.36 14.00 1.64 2.280 14.465 17.214 3.897 Individual atomic B min max mean iso aniso Overall: 5.52 67.88 15.21 1.06 503 3271 Protein: 5.52 35.68 10.71 1.06 0 2902 Water: 6.68 67.88 30.21 N/A 503 367 Other: 13.85 28.13 20.99 N/A 0 2 Chain A: 5.58 55.01 12.73 N/A 0 1624 Chain B: 5.52 67.88 12.50 N/A 0 1647 Chain S: 13.30 62.44 32.13 N/A 503 0 Histogram: Values Number of atoms 5.52 - 11.75 2134 11.75 - 17.99 689 17.99 - 24.23 292 24.23 - 30.46 238 30.46 - 36.70 169 36.70 - 42.94 148 42.94 - 49.17 69 49.17 - 55.41 25 55.41 - 61.65 6 61.65 - 67.88 4 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1400 r_work=0.1236 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1401 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1391 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1391 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891194 | | target function (ml) not normalized (work): 728812.788226 | | target function (ml) not normalized (free): 15226.948158 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1391 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1446 0.1446 0.1488 n_refl.: 191139 remove outliers: r(all,work,free)=0.1446 0.1446 0.1488 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1440 0.1484 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1226 0.1385 n_refl.: 191139 remove outliers: r(all,work,free)=0.1229 0.1226 0.1385 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3787 398.008 362.214 0.427 0.945 0.251 13.296-10.522 98.02 98 1 0.2353 528.900 510.867 0.716 0.947 0.214 10.503-8.327 98.35 176 3 0.1987 555.265 556.766 0.885 0.947 0.177 8.318-6.595 100.00 360 8 0.2097 414.736 410.039 0.901 0.946 0.138 6.588-5.215 100.00 711 7 0.1845 381.101 370.079 0.889 0.946 0.120 5.214-4.128 98.38 1367 28 0.1172 557.435 552.092 0.973 0.947 0.090 4.126-3.266 94.74 2603 46 0.1101 508.132 500.962 1.032 0.947 0.009 3.266-2.585 99.86 5447 97 0.1093 342.774 339.079 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0970 258.603 255.699 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.400 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.485 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.322 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1012 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1385 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1385 | n_water=870 | time (s): 2.850 (total time: 2.850) Filter (dist) r_work=0.1226 r_free=0.1384 | n_water=869 | time (s): 110.390 (total time: 113.240) Filter (q & B) r_work=0.1226 r_free=0.1382 | n_water=856 | time (s): 5.150 (total time: 118.390) Compute maps r_work=0.1226 r_free=0.1382 | n_water=856 | time (s): 1.770 (total time: 120.160) Filter (map) r_work=0.1250 r_free=0.1384 | n_water=713 | time (s): 4.550 (total time: 124.710) Find peaks r_work=0.1250 r_free=0.1384 | n_water=713 | time (s): 0.820 (total time: 125.530) Add new water r_work=0.1267 r_free=0.1404 | n_water=963 | time (s): 4.670 (total time: 130.200) Refine new water occ: r_work=0.1217 r_free=0.1361 adp: r_work=0.1209 r_free=0.1359 occ: r_work=0.1206 r_free=0.1359 adp: r_work=0.1206 r_free=0.1358 occ: r_work=0.1204 r_free=0.1358 adp: r_work=0.1204 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1358 r_work=0.1204 r_free=0.1358 | n_water=963 | time (s): 335.950 (total time: 466.150) Filter (q & B) r_work=0.1208 r_free=0.1361 | n_water=867 | time (s): 4.330 (total time: 470.480) Filter (dist only) r_work=0.1209 r_free=0.1360 | n_water=865 | time (s): 110.900 (total time: 581.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.589769 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.309507 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1360 0.0153 0.036 1.1 5.8 0.0 0.3 0 0.795 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.60 1.53 1.824 14.125 15.310 3.873 12.01 13.59 1.58 1.891 14.103 15.310 3.866 Individual atomic B min max mean iso aniso Overall: 5.53 67.51 14.89 1.00 499 3270 Protein: 5.53 33.00 10.66 1.00 0 2902 Water: 5.86 67.51 29.06 N/A 499 366 Other: 13.89 27.32 20.61 N/A 0 2 Chain A: 5.53 54.12 12.61 N/A 0 1623 Chain B: 5.53 67.51 12.43 N/A 0 1647 Chain S: 5.86 62.39 30.41 N/A 499 0 Histogram: Values Number of atoms 5.53 - 11.73 2129 11.73 - 17.93 713 17.93 - 24.13 312 24.13 - 30.32 246 30.32 - 36.52 155 36.52 - 42.72 122 42.72 - 48.92 65 48.92 - 55.12 20 55.12 - 61.32 4 61.32 - 67.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1359 r_work=0.1201 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1359 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864391 | | target function (ml) not normalized (work): 723773.326486 | | target function (ml) not normalized (free): 15141.406231 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1429 0.1428 0.1476 n_refl.: 191134 remove outliers: r(all,work,free)=0.1429 0.1428 0.1476 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1421 0.1421 0.1471 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191134 remove outliers: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3778 352.816 316.391 0.412 0.946 0.247 13.296-10.522 96.04 96 1 0.2346 480.500 452.619 0.711 0.947 0.225 10.503-8.327 98.35 176 3 0.2067 502.866 498.388 0.867 0.947 0.220 8.318-6.595 100.00 360 8 0.2195 375.599 370.758 0.890 0.947 0.110 6.588-5.215 100.00 711 7 0.1902 345.138 335.088 0.889 0.947 0.110 5.214-4.128 98.38 1367 28 0.1196 504.832 499.363 0.975 0.947 0.080 4.126-3.266 94.74 2603 46 0.1120 460.181 453.818 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1088 310.427 307.222 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0942 234.200 231.730 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0914 138.611 137.330 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0990 74.620 73.900 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.030 38.373 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1173 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1197 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1356 | n_water=865 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1198 r_free=0.1356 | n_water=864 | time (s): 106.420 (total time: 108.760) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=854 | time (s): 5.220 (total time: 113.980) Compute maps r_work=0.1198 r_free=0.1356 | n_water=854 | time (s): 2.270 (total time: 116.250) Filter (map) r_work=0.1222 r_free=0.1368 | n_water=727 | time (s): 5.040 (total time: 121.290) Find peaks r_work=0.1222 r_free=0.1368 | n_water=727 | time (s): 0.590 (total time: 121.880) Add new water r_work=0.1235 r_free=0.1384 | n_water=963 | time (s): 4.350 (total time: 126.230) Refine new water occ: r_work=0.1196 r_free=0.1351 adp: r_work=0.1196 r_free=0.1352 occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1194 r_free=0.1351 occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 | n_water=963 | time (s): 189.140 (total time: 315.370) Filter (q & B) r_work=0.1196 r_free=0.1348 | n_water=889 | time (s): 5.030 (total time: 320.400) Filter (dist only) r_work=0.1196 r_free=0.1348 | n_water=888 | time (s): 111.010 (total time: 431.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500038 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.868263 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1353 0.0154 0.037 1.1 8.0 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.53 1.54 1.791 14.116 15.868 3.766 12.01 13.54 1.53 1.889 14.077 15.868 3.761 Individual atomic B min max mean iso aniso Overall: 5.54 67.04 14.90 0.96 522 3270 Protein: 5.54 31.74 10.57 0.96 0 2902 Water: 5.96 67.04 29.02 N/A 522 366 Other: 13.82 25.72 19.77 N/A 0 2 Chain A: 5.59 52.85 12.49 N/A 0 1623 Chain B: 5.54 67.04 12.32 N/A 0 1647 Chain S: 5.96 62.42 30.53 N/A 522 0 Histogram: Values Number of atoms 5.54 - 11.69 2135 11.69 - 17.84 730 17.84 - 23.99 299 23.99 - 30.14 241 30.14 - 36.29 161 36.29 - 42.44 136 42.44 - 48.59 66 48.59 - 54.74 18 54.74 - 60.89 3 60.89 - 67.04 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1354 r_work=0.1201 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1354 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760035 | | target function (ml) not normalized (work): 704213.287146 | | target function (ml) not normalized (free): 14751.737918 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1473 n_refl.: 191130 remove outliers: r(all,work,free)=0.1409 0.1408 0.1473 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1468 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3882 352.816 313.553 0.386 0.950 0.224 13.296-10.522 96.04 96 1 0.2393 480.500 460.756 0.712 0.952 0.215 10.503-8.327 98.35 176 3 0.2073 502.866 496.900 0.861 0.952 0.210 8.318-6.595 100.00 360 8 0.2183 375.599 369.940 0.887 0.952 0.119 6.588-5.215 100.00 711 7 0.1938 345.138 334.881 0.883 0.952 0.097 5.214-4.128 98.38 1367 28 0.1208 504.832 498.900 0.970 0.952 0.070 4.126-3.266 94.74 2603 46 0.1140 460.181 453.338 1.030 0.952 0.000 3.266-2.585 99.86 5447 97 0.1109 310.427 307.157 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0945 234.200 231.656 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0910 138.611 137.312 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0978 74.620 73.903 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.030 38.361 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1254 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1356 | n_water=888 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1197 r_free=0.1356 | n_water=885 | time (s): 114.440 (total time: 116.820) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=873 | time (s): 5.630 (total time: 122.450) Compute maps r_work=0.1198 r_free=0.1356 | n_water=873 | time (s): 2.040 (total time: 124.490) Filter (map) r_work=0.1221 r_free=0.1357 | n_water=746 | time (s): 4.340 (total time: 128.830) Find peaks r_work=0.1221 r_free=0.1357 | n_water=746 | time (s): 0.580 (total time: 129.410) Add new water r_work=0.1233 r_free=0.1370 | n_water=971 | time (s): 4.840 (total time: 134.250) Refine new water occ: r_work=0.1197 r_free=0.1340 adp: r_work=0.1197 r_free=0.1341 occ: r_work=0.1195 r_free=0.1338 adp: r_work=0.1195 r_free=0.1339 occ: r_work=0.1193 r_free=0.1337 adp: r_work=0.1192 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1338 r_work=0.1192 r_free=0.1338 | n_water=971 | time (s): 283.790 (total time: 418.040) Filter (q & B) r_work=0.1196 r_free=0.1346 | n_water=900 | time (s): 4.640 (total time: 422.680) Filter (dist only) r_work=0.1197 r_free=0.1346 | n_water=899 | time (s): 116.220 (total time: 538.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574186 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.720992 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1354 0.0156 0.037 1.1 9.5 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.54 1.56 1.758 14.033 13.721 3.760 12.01 13.56 1.55 1.753 14.037 13.721 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 66.98 14.93 0.94 534 3269 Protein: 5.56 31.57 10.55 0.94 0 2902 Water: 6.09 66.98 29.05 N/A 534 365 Other: 13.77 25.67 19.72 N/A 0 2 Chain A: 5.64 52.74 12.46 N/A 0 1623 Chain B: 5.56 66.98 12.28 N/A 0 1646 Chain S: 6.09 62.38 30.63 N/A 534 0 Histogram: Values Number of atoms 5.56 - 11.70 2142 11.70 - 17.84 727 17.84 - 23.99 302 23.99 - 30.13 238 30.13 - 36.27 162 36.27 - 42.41 138 42.41 - 48.55 69 48.55 - 54.69 19 54.69 - 60.83 3 60.83 - 66.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1356 r_work=0.1201 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1356 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759112 | | target function (ml) not normalized (work): 704040.281103 | | target function (ml) not normalized (free): 14745.265681 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1482 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1406 0.1482 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1400 0.1398 0.1477 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1201 0.1198 0.1358 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3896 348.147 314.142 0.348 0.950 0.160 13.296-10.522 96.04 96 1 0.2399 480.500 460.535 0.692 0.951 0.160 10.503-8.327 98.35 176 3 0.2160 502.866 496.109 0.861 0.952 0.160 8.315-6.595 100.00 359 8 0.2137 374.653 370.818 0.889 0.952 0.123 6.588-5.215 100.00 711 7 0.1931 345.138 335.289 0.884 0.952 0.100 5.214-4.128 98.38 1367 28 0.1218 504.832 499.087 0.973 0.952 0.080 4.126-3.266 94.74 2603 46 0.1142 460.181 453.307 1.033 0.952 0.000 3.266-2.585 99.86 5447 97 0.1114 310.427 307.078 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0952 234.200 231.623 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0911 138.611 137.310 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0974 74.620 73.904 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.030 38.353 1.039 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1333 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1358 | n_water=899 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1198 r_free=0.1358 | n_water=899 | time (s): 109.840 (total time: 112.440) Filter (q & B) r_work=0.1199 r_free=0.1358 | n_water=888 | time (s): 5.020 (total time: 117.460) Compute maps r_work=0.1199 r_free=0.1358 | n_water=888 | time (s): 2.210 (total time: 119.670) Filter (map) r_work=0.1221 r_free=0.1354 | n_water=754 | time (s): 4.660 (total time: 124.330) Find peaks r_work=0.1221 r_free=0.1354 | n_water=754 | time (s): 0.540 (total time: 124.870) Add new water r_work=0.1232 r_free=0.1362 | n_water=956 | time (s): 4.890 (total time: 129.760) Refine new water occ: r_work=0.1199 r_free=0.1342 adp: r_work=0.1199 r_free=0.1343 occ: r_work=0.1196 r_free=0.1341 adp: r_work=0.1196 r_free=0.1342 occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1194 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1341 r_work=0.1194 r_free=0.1341 | n_water=956 | time (s): 207.960 (total time: 337.720) Filter (q & B) r_work=0.1197 r_free=0.1346 | n_water=897 | time (s): 4.990 (total time: 342.710) Filter (dist only) r_work=0.1198 r_free=0.1346 | n_water=896 | time (s): 114.260 (total time: 456.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.559133 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.169348 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1346 0.0146 0.037 1.1 8.4 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.46 1.46 1.748 13.985 14.169 3.759 12.02 13.51 1.49 1.836 13.960 14.169 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 66.18 14.82 0.90 531 3269 Protein: 5.57 29.65 10.47 0.90 0 2902 Water: 6.36 66.18 28.89 N/A 531 365 Other: 13.81 23.67 18.74 N/A 0 2 Chain A: 5.68 51.32 12.35 N/A 0 1623 Chain B: 5.57 66.18 12.18 N/A 0 1646 Chain S: 6.36 62.38 30.55 N/A 531 0 Histogram: Values Number of atoms 5.57 - 11.63 2126 11.63 - 17.69 764 17.69 - 23.75 282 23.75 - 29.81 223 29.81 - 35.87 178 35.87 - 41.94 133 41.94 - 48.00 64 48.00 - 54.06 23 54.06 - 60.12 4 60.12 - 66.18 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1351 r_work=0.1202 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1351 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1353 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757447 | | target function (ml) not normalized (work): 703720.998862 | | target function (ml) not normalized (free): 14730.859582 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1408 0.1406 0.1489 n_refl.: 191128 remove outliers: r(all,work,free)=0.1408 0.1406 0.1489 n_refl.: 191128 overall B=-0.22 to atoms: r(all,work,free)=0.1373 0.1372 0.1466 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1354 n_refl.: 191128 remove outliers: r(all,work,free)=0.1203 0.1200 0.1354 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3906 348.147 310.447 0.348 0.951 0.149 13.296-10.522 96.04 96 1 0.2414 480.500 460.242 0.704 0.952 0.142 10.503-8.327 98.35 176 3 0.2209 502.866 494.483 0.882 0.953 0.137 8.315-6.595 100.00 359 8 0.2137 374.653 370.880 0.908 0.953 0.113 6.588-5.215 100.00 711 7 0.1930 345.138 335.565 0.905 0.953 0.092 5.214-4.128 98.38 1367 28 0.1219 504.832 499.185 0.997 0.953 0.090 4.126-3.266 94.74 2603 46 0.1144 460.181 453.402 1.057 0.953 0.000 3.266-2.585 99.86 5447 97 0.1117 310.427 307.199 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0959 234.200 231.607 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.611 137.334 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0973 74.620 73.914 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.030 38.355 1.025 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0490 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1354 | n_water=896 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1200 r_free=0.1355 | n_water=895 | time (s): 112.230 (total time: 115.220) Filter (q & B) r_work=0.1201 r_free=0.1354 | n_water=886 | time (s): 4.080 (total time: 119.300) Compute maps r_work=0.1201 r_free=0.1354 | n_water=886 | time (s): 1.910 (total time: 121.210) Filter (map) r_work=0.1223 r_free=0.1360 | n_water=761 | time (s): 4.380 (total time: 125.590) Find peaks r_work=0.1223 r_free=0.1360 | n_water=761 | time (s): 0.630 (total time: 126.220) Add new water r_work=0.1233 r_free=0.1368 | n_water=966 | time (s): 4.090 (total time: 130.310) Refine new water occ: r_work=0.1200 r_free=0.1344 adp: r_work=0.1200 r_free=0.1343 occ: r_work=0.1198 r_free=0.1344 adp: r_work=0.1198 r_free=0.1344 occ: r_work=0.1196 r_free=0.1344 adp: r_work=0.1195 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1344 r_work=0.1195 r_free=0.1344 | n_water=966 | time (s): 210.160 (total time: 340.470) Filter (q & B) r_work=0.1199 r_free=0.1351 | n_water=895 | time (s): 5.270 (total time: 345.740) Filter (dist only) r_work=0.1200 r_free=0.1351 | n_water=894 | time (s): 113.070 (total time: 458.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607946 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.248122 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1366 0.0163 0.038 1.1 7.5 0.0 0.3 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.66 1.63 1.716 13.679 14.248 3.759 12.04 13.68 1.64 1.770 13.660 14.248 3.757 Individual atomic B min max mean iso aniso Overall: 5.38 64.92 14.52 0.88 529 3269 Protein: 5.38 28.47 10.23 0.88 0 2902 Water: 5.84 64.92 28.44 N/A 529 365 Other: 13.64 22.05 17.84 N/A 0 2 Chain A: 5.46 50.80 12.08 N/A 0 1623 Chain B: 5.38 64.92 11.92 N/A 0 1646 Chain S: 5.84 62.18 30.13 N/A 529 0 Histogram: Values Number of atoms 5.38 - 11.34 2106 11.34 - 17.29 784 17.29 - 23.24 273 23.24 - 29.20 218 29.20 - 35.15 190 35.15 - 41.10 125 41.10 - 47.06 67 47.06 - 53.01 28 53.01 - 58.96 4 58.96 - 64.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1368 r_work=0.1204 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1368 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1368 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756677 | | target function (ml) not normalized (work): 703576.766870 | | target function (ml) not normalized (free): 14739.722920 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1368 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1380 0.1379 0.1475 n_refl.: 191128 remove outliers: r(all,work,free)=0.1380 0.1379 0.1475 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1380 0.1379 0.1475 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3788 348.147 309.385 0.402 0.906 0.215 13.296-10.522 96.04 96 1 0.2378 480.500 461.648 0.739 0.908 0.157 10.503-8.327 98.35 176 3 0.2209 502.866 494.449 0.913 0.908 0.132 8.315-6.595 100.00 359 8 0.2144 374.653 370.333 0.941 0.908 0.104 6.588-5.215 100.00 711 7 0.1939 345.138 335.074 0.941 0.909 0.090 5.214-4.128 98.38 1367 28 0.1237 504.832 498.718 1.037 0.909 0.067 4.126-3.266 94.74 2603 46 0.1162 460.181 452.619 1.099 0.910 0.005 3.266-2.585 99.86 5447 97 0.1125 310.427 306.878 1.080 0.911 0.000 2.585-2.046 97.45 10613 204 0.0963 234.200 231.488 1.087 0.913 0.000 2.046-1.619 99.39 21536 464 0.0907 138.611 137.255 1.102 0.915 0.000 1.619-1.281 98.00 42464 925 0.0949 74.620 73.959 1.086 0.920 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.030 38.329 1.044 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1229 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1360 | n_water=894 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1193 r_free=0.1360 | n_water=892 | time (s): 109.800 (total time: 112.930) Filter (q & B) r_work=0.1194 r_free=0.1361 | n_water=880 | time (s): 5.060 (total time: 117.990) Compute maps r_work=0.1194 r_free=0.1361 | n_water=880 | time (s): 1.890 (total time: 119.880) Filter (map) r_work=0.1216 r_free=0.1355 | n_water=752 | time (s): 5.230 (total time: 125.110) Find peaks r_work=0.1216 r_free=0.1355 | n_water=752 | time (s): 0.890 (total time: 126.000) Add new water r_work=0.1225 r_free=0.1365 | n_water=975 | time (s): 4.450 (total time: 130.450) Refine new water occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1189 r_free=0.1344 adp: r_work=0.1189 r_free=0.1344 occ: r_work=0.1187 r_free=0.1345 adp: r_work=0.1187 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1345 r_work=0.1187 r_free=0.1345 | n_water=975 | time (s): 161.790 (total time: 292.240) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=903 | time (s): 4.490 (total time: 296.730) Filter (dist only) r_work=0.1191 r_free=0.1349 | n_water=902 | time (s): 117.050 (total time: 413.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.543655 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.461757 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1354 0.0159 0.038 1.1 5.1 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.54 1.59 1.674 13.630 13.462 3.755 11.96 13.55 1.59 1.675 13.627 13.462 3.755 Individual atomic B min max mean iso aniso Overall: 5.40 64.68 14.52 0.86 537 3269 Protein: 5.40 28.30 10.25 0.86 0 2902 Water: 5.84 64.68 28.27 N/A 537 365 Other: 13.63 22.07 17.85 N/A 0 2 Chain A: 5.48 50.73 12.07 N/A 0 1623 Chain B: 5.40 64.68 11.92 N/A 0 1646 Chain S: 5.84 62.17 29.95 N/A 537 0 Histogram: Values Number of atoms 5.40 - 11.33 2095 11.33 - 17.25 797 17.25 - 23.18 280 23.18 - 29.11 224 29.11 - 35.04 179 35.04 - 40.97 123 40.97 - 46.90 73 46.90 - 52.82 27 52.82 - 58.75 5 58.75 - 64.68 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1355 r_work=0.1196 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1355 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754907 | | target function (ml) not normalized (work): 703245.264845 | | target function (ml) not normalized (free): 14731.632198 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1385 0.1383 0.1485 n_refl.: 191128 remove outliers: r(all,work,free)=0.1385 0.1383 0.1485 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1385 0.1383 0.1485 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3808 348.147 308.264 0.361 0.995 0.208 13.296-10.522 96.04 96 1 0.2394 480.500 460.452 0.667 0.997 0.146 10.503-8.327 98.35 176 3 0.2243 502.866 493.028 0.832 0.997 0.120 8.315-6.595 100.00 359 8 0.2156 374.653 369.728 0.856 0.997 0.103 6.588-5.215 100.00 711 7 0.1961 345.138 334.696 0.855 0.998 0.090 5.214-4.128 98.38 1367 28 0.1242 504.832 498.921 0.943 0.999 0.049 4.126-3.266 94.74 2603 46 0.1164 460.181 452.600 1.002 1.000 0.005 3.266-2.585 99.86 5447 97 0.1124 310.427 306.969 0.984 1.001 0.000 2.585-2.046 97.45 10613 204 0.0963 234.200 231.470 0.991 1.003 0.000 2.046-1.619 99.39 21536 464 0.0910 138.611 137.275 1.005 1.006 0.000 1.619-1.281 98.00 42464 925 0.0948 74.620 73.960 0.992 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.030 38.315 0.956 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0882 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1194 r_free=0.1358 After: r_work=0.1194 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1361 | n_water=902 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1195 r_free=0.1361 | n_water=902 | time (s): 113.950 (total time: 116.380) Filter (q & B) r_work=0.1196 r_free=0.1361 | n_water=893 | time (s): 4.580 (total time: 120.960) Compute maps r_work=0.1196 r_free=0.1361 | n_water=893 | time (s): 2.040 (total time: 123.000) Filter (map) r_work=0.1219 r_free=0.1365 | n_water=769 | time (s): 4.350 (total time: 127.350) Find peaks r_work=0.1219 r_free=0.1365 | n_water=769 | time (s): 0.560 (total time: 127.910) Add new water r_work=0.1227 r_free=0.1375 | n_water=986 | time (s): 4.060 (total time: 131.970) Refine new water occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1193 r_free=0.1351 occ: r_work=0.1191 r_free=0.1351 adp: r_work=0.1191 r_free=0.1352 occ: r_work=0.1189 r_free=0.1352 adp: r_work=0.1189 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1352 r_work=0.1189 r_free=0.1352 | n_water=986 | time (s): 262.120 (total time: 394.090) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=909 | time (s): 4.880 (total time: 398.970) Filter (dist only) r_work=0.1194 r_free=0.1361 | n_water=908 | time (s): 114.280 (total time: 513.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560966 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.442013 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1369 0.0169 0.039 1.2 8.7 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.69 1.69 1.669 13.649 14.442 3.761 11.98 13.69 1.71 1.672 13.649 14.442 3.757 Individual atomic B min max mean iso aniso Overall: 5.44 63.92 14.55 0.87 543 3269 Protein: 5.44 28.21 10.26 0.87 0 2902 Water: 5.90 63.92 28.25 N/A 543 365 Other: 13.69 21.95 17.82 N/A 0 2 Chain A: 5.53 50.45 12.06 N/A 0 1623 Chain B: 5.44 63.92 11.91 N/A 0 1646 Chain S: 5.90 62.14 30.02 N/A 543 0 Histogram: Values Number of atoms 5.44 - 11.29 2075 11.29 - 17.13 816 17.13 - 22.98 276 22.98 - 28.83 221 28.83 - 34.68 190 34.68 - 40.53 114 40.53 - 46.37 83 46.37 - 52.22 28 52.22 - 58.07 4 58.07 - 63.92 5 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1369 r_work=0.1198 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1369 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1370 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757129 | | target function (ml) not normalized (work): 703661.399944 | | target function (ml) not normalized (free): 14741.558201 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1365 0.1480 5.6858 5.7523| | 2: 2.94 - 2.33 1.00 7339 128 0.1070 0.1372 5.0726 5.1728| | 3: 2.33 - 2.04 0.96 6939 150 0.0910 0.1233 4.6614 4.7728| | 4: 2.04 - 1.85 1.00 7170 155 0.0905 0.1047 4.3977 4.5566| | 5: 1.85 - 1.72 0.99 7113 159 0.0938 0.1005 4.1568 4.2463| | 6: 1.72 - 1.62 0.99 7102 142 0.0900 0.1102 3.9536 4.0902| | 7: 1.62 - 1.54 0.99 7104 148 0.0902 0.0975 3.8069 3.9349| | 8: 1.54 - 1.47 0.96 6798 152 0.0899 0.1343 3.7081 3.9128| | 9: 1.47 - 1.41 0.98 6938 155 0.0931 0.1121 3.6272 3.7484| | 10: 1.41 - 1.36 0.99 7022 150 0.0980 0.1210 3.5606 3.6792| | 11: 1.36 - 1.32 0.99 6997 151 0.1000 0.1132 3.491 3.5946| | 12: 1.32 - 1.28 0.98 6975 149 0.1041 0.1131 3.4644 3.5899| | 13: 1.28 - 1.25 0.98 6907 166 0.1054 0.1276 3.4466 3.5866| | 14: 1.25 - 1.22 0.98 7015 112 0.1113 0.1599 3.4385 3.6851| | 15: 1.22 - 1.19 0.98 6956 137 0.1174 0.1254 3.4519 3.4965| | 16: 1.19 - 1.17 0.93 6604 132 0.1254 0.1536 3.4668 3.6485| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1241 3.4345 3.4497| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1713 3.4389 3.5332| | 19: 1.12 - 1.10 0.97 6948 106 0.1473 0.1772 3.4213 3.5973| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1591 3.4104 3.4368| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2157 3.4186 3.5093| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1957 3.4131 3.4157| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2016 3.4336 3.4894| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2279 3.436 3.5179| | 25: 1.02 - 1.01 0.93 6552 130 0.2618 0.2503 3.4498 3.5218| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2846 3.4156 3.4211| | 27: 0.99 - 0.98 0.94 6647 131 0.3045 0.2795 3.47 3.3952| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.39 1.00 0.97 10736.56| | 2: 2.94 - 2.33 7339 128 0.93 12.63 0.99 0.97 5009.17| | 3: 2.33 - 2.04 6939 150 0.96 7.78 1.01 0.97 1737.33| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.97 1017.51| | 5: 1.85 - 1.72 7113 159 0.96 8.13 1.00 0.97 641.87| | 6: 1.72 - 1.62 7102 142 0.96 8.12 1.00 0.98 450.95| | 7: 1.62 - 1.54 7104 148 0.96 8.22 1.01 0.99 342.12| | 8: 1.54 - 1.47 6798 152 0.96 8.34 1.01 0.99 282.98| | 9: 1.47 - 1.41 6938 155 0.96 8.50 1.00 0.99 232.26| | 10: 1.41 - 1.36 7022 150 0.96 8.94 1.00 0.98 203.93| | 11: 1.36 - 1.32 6997 151 0.96 9.03 0.99 0.97 177.22| | 12: 1.32 - 1.28 6975 149 0.96 9.14 0.98 0.96 164.21| | 13: 1.28 - 1.25 6907 166 0.95 9.74 1.01 0.97 162.20| | 14: 1.25 - 1.22 7015 112 0.95 10.88 1.02 0.98 166.62| | 15: 1.22 - 1.19 6956 137 0.94 11.37 1.01 0.99 169.13| | 16: 1.19 - 1.17 6604 132 0.95 11.51 1.01 0.98 161.54| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.98 154.80| | 18: 1.14 - 1.12 6875 142 0.94 12.78 1.01 0.96 148.39| | 19: 1.12 - 1.10 6948 106 0.93 14.20 1.00 0.96 152.11| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.95 151.25| | 21: 1.08 - 1.07 6852 152 0.91 16.71 1.00 0.94 154.35| | 22: 1.07 - 1.05 6836 135 0.89 18.37 0.99 0.94 155.97| | 23: 1.05 - 1.03 6827 159 0.87 20.57 0.99 0.93 165.74| | 24: 1.03 - 1.02 6784 133 0.85 23.23 0.99 0.94 180.02| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.97 0.91 182.42| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.89 176.35| | 27: 0.99 - 0.98 6647 131 0.82 26.22 0.98 0.88 160.11| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 148.39 max = 10736.56 mean = 906.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.93 mean = 13.34| |phase err.(test): min = 0.00 max = 88.56 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1370 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1394 0.1393 0.1498 n_refl.: 191128 remove outliers: r(all,work,free)=0.1394 0.1393 0.1498 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1394 0.1393 0.1498 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1369 n_refl.: 191128 remove outliers: r(all,work,free)=0.1200 0.1196 0.1369 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3799 348.147 309.190 0.384 0.909 0.190 13.296-10.522 96.04 96 1 0.2412 480.500 459.832 0.723 0.911 0.135 10.503-8.327 98.35 176 3 0.2217 502.866 494.620 0.909 0.912 0.109 8.315-6.595 100.00 359 8 0.2148 374.653 369.810 0.935 0.912 0.094 6.588-5.215 100.00 711 7 0.1951 345.138 334.713 0.934 0.912 0.090 5.214-4.128 98.38 1367 28 0.1243 504.832 498.679 1.034 0.913 0.090 4.126-3.266 94.74 2603 46 0.1171 460.181 452.321 1.096 0.914 0.000 3.266-2.585 99.86 5447 97 0.1125 310.427 306.935 1.078 0.915 0.000 2.585-2.046 97.45 10613 204 0.0966 234.200 231.521 1.084 0.917 0.000 2.046-1.619 99.39 21536 464 0.0915 138.611 137.266 1.100 0.921 0.000 1.619-1.281 98.00 42464 925 0.0953 74.620 73.957 1.087 0.926 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.030 38.314 1.049 0.936 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0563 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2040 0.1997 0.082 5.170 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1942 0.082 5.170 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1942 0.082 5.170 5.2 78.0 14.6 805 0.000 1_nqh: 0.1806 0.1943 0.082 5.170 5.2 78.0 14.6 805 0.002 1_weight: 0.1806 0.1943 0.082 5.170 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1507 0.039 1.166 5.2 78.0 14.6 805 0.158 1_adp: 0.1301 0.1576 0.039 1.166 5.3 73.0 15.0 805 0.158 1_regHadp: 0.1300 0.1572 0.039 1.166 5.3 73.0 15.0 805 0.158 1_occ: 0.1286 0.1562 0.039 1.166 5.3 73.0 15.0 805 0.158 2_bss: 0.1277 0.1550 0.039 1.166 5.4 73.2 15.2 805 0.158 2_settarget: 0.1277 0.1550 0.039 1.166 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1277 0.1550 0.039 1.177 5.4 73.2 15.2 805 0.158 2_nqh: 0.1277 0.1550 0.039 1.177 5.4 73.2 15.2 805 0.158 2_sol: 0.1275 0.1513 0.039 1.177 5.4 73.2 16.2 884 n/a 2_weight: 0.1275 0.1513 0.039 1.177 5.4 73.2 16.2 884 n/a 2_xyzrec: 0.1260 0.1532 0.042 1.135 5.4 73.2 16.2 884 n/a 2_adp: 0.1239 0.1520 0.042 1.135 5.3 68.5 16.3 884 n/a 2_regHadp: 0.1239 0.1522 0.042 1.135 5.3 68.5 16.3 884 n/a 2_occ: 0.1232 0.1517 0.042 1.135 5.3 68.5 16.3 884 n/a 3_bss: 0.1238 0.1523 0.042 1.135 5.3 68.4 16.3 884 n/a 3_settarget: 0.1238 0.1523 0.042 1.135 5.3 68.4 16.3 884 n/a 3_updatecdl: 0.1238 0.1523 0.042 1.137 5.3 68.4 16.3 884 n/a 3_nqh: 0.1238 0.1523 0.042 1.137 5.3 68.4 16.3 884 n/a 3_sol: 0.1255 0.1519 0.042 1.137 5.3 68.4 15.4 870 n/a 3_weight: 0.1255 0.1519 0.042 1.137 5.3 68.4 15.4 870 n/a 3_xyzrec: 0.1243 0.1444 0.035 1.101 5.3 68.4 15.4 870 n/a 3_adp: 0.1236 0.1400 0.035 1.101 5.5 67.9 15.2 870 n/a 3_regHadp: 0.1236 0.1401 0.035 1.101 5.5 67.9 15.2 870 n/a 3_occ: 0.1230 0.1391 0.035 1.101 5.5 67.9 15.2 870 n/a 4_bss: 0.1226 0.1385 0.035 1.101 5.5 67.9 15.2 870 n/a 4_settarget: 0.1226 0.1385 0.035 1.101 5.5 67.9 15.2 870 n/a 4_updatecdl: 0.1226 0.1385 0.035 1.101 5.5 67.9 15.2 870 n/a 4_nqh: 0.1226 0.1385 0.035 1.101 5.5 67.9 15.2 870 n/a 4_sol: 0.1209 0.1360 0.035 1.101 5.5 67.9 14.9 865 n/a 4_weight: 0.1209 0.1360 0.035 1.101 5.5 67.9 14.9 865 n/a 4_xyzrec: 0.1206 0.1360 0.036 1.121 5.5 67.9 14.9 865 n/a 4_adp: 0.1201 0.1359 0.036 1.121 5.5 67.5 14.9 865 n/a 4_regHadp: 0.1201 0.1359 0.036 1.121 5.5 67.5 14.9 865 n/a 4_occ: 0.1199 0.1358 0.036 1.121 5.5 67.5 14.9 865 n/a 5_bss: 0.1197 0.1357 0.036 1.121 5.5 67.5 14.9 865 n/a 5_settarget: 0.1197 0.1357 0.036 1.121 5.5 67.5 14.9 865 n/a 5_updatecdl: 0.1197 0.1357 0.036 1.121 5.5 67.5 14.9 865 n/a 5_nqh: 0.1197 0.1356 0.036 1.121 5.5 67.5 14.9 865 n/a 5_sol: 0.1196 0.1348 0.036 1.121 5.5 67.5 15.0 888 n/a 5_weight: 0.1196 0.1348 0.036 1.121 5.5 67.5 15.0 888 n/a 5_xyzrec: 0.1199 0.1353 0.037 1.118 5.5 67.5 15.0 888 n/a 5_adp: 0.1201 0.1354 0.037 1.118 5.5 67.0 14.9 888 n/a 5_regHadp: 0.1201 0.1354 0.037 1.118 5.5 67.0 14.9 888 n/a 5_occ: 0.1198 0.1359 0.037 1.118 5.5 67.0 14.9 888 n/a 6_bss: 0.1197 0.1356 0.037 1.118 5.5 67.0 14.9 888 n/a 6_settarget: 0.1197 0.1356 0.037 1.118 5.5 67.0 14.9 888 n/a 6_updatecdl: 0.1197 0.1356 0.037 1.119 5.5 67.0 14.9 888 n/a 6_nqh: 0.1197 0.1356 0.037 1.119 5.5 67.0 14.9 888 n/a 6_sol: 0.1197 0.1346 0.037 1.119 5.5 67.0 14.9 899 n/a 6_weight: 0.1197 0.1346 0.037 1.119 5.5 67.0 14.9 899 n/a 6_xyzrec: 0.1199 0.1354 0.037 1.134 5.5 67.0 14.9 899 n/a 6_adp: 0.1201 0.1356 0.037 1.134 5.6 67.0 14.9 899 n/a 6_regHadp: 0.1201 0.1356 0.037 1.134 5.6 67.0 14.9 899 n/a 6_occ: 0.1199 0.1360 0.037 1.134 5.6 67.0 14.9 899 n/a 7_bss: 0.1198 0.1358 0.037 1.134 5.5 66.9 14.9 899 n/a 7_settarget: 0.1198 0.1358 0.037 1.134 5.5 66.9 14.9 899 n/a 7_updatecdl: 0.1198 0.1358 0.037 1.134 5.5 66.9 14.9 899 n/a 7_nqh: 0.1198 0.1358 0.037 1.134 5.5 66.9 14.9 899 n/a 7_sol: 0.1198 0.1346 0.037 1.134 5.5 66.9 14.9 896 n/a 7_weight: 0.1198 0.1346 0.037 1.134 5.5 66.9 14.9 896 n/a 7_xyzrec: 0.1200 0.1346 0.037 1.129 5.5 66.9 14.9 896 n/a 7_adp: 0.1202 0.1351 0.037 1.129 5.6 66.2 14.8 896 n/a 7_regHadp: 0.1202 0.1351 0.037 1.129 5.6 66.2 14.8 896 n/a 7_occ: 0.1201 0.1353 0.037 1.129 5.6 66.2 14.8 896 n/a 8_bss: 0.1200 0.1354 0.037 1.129 5.3 66.0 14.6 896 n/a 8_settarget: 0.1200 0.1354 0.037 1.129 5.3 66.0 14.6 896 n/a 8_updatecdl: 0.1200 0.1354 0.037 1.130 5.3 66.0 14.6 896 n/a 8_nqh: 0.1200 0.1354 0.037 1.130 5.3 66.0 14.6 896 n/a 8_sol: 0.1200 0.1351 0.037 1.130 5.3 66.0 14.6 894 n/a 8_weight: 0.1200 0.1351 0.037 1.130 5.3 66.0 14.6 894 n/a 8_xyzrec: 0.1202 0.1366 0.038 1.136 5.3 66.0 14.6 894 n/a 8_adp: 0.1204 0.1368 0.038 1.136 5.4 64.9 14.5 894 n/a 8_regHadp: 0.1204 0.1368 0.038 1.136 5.4 64.9 14.5 894 n/a 8_occ: 0.1202 0.1368 0.038 1.136 5.4 64.9 14.5 894 n/a 9_bss: 0.1193 0.1360 0.038 1.136 5.4 64.9 14.5 894 n/a 9_settarget: 0.1193 0.1360 0.038 1.136 5.4 64.9 14.5 894 n/a 9_updatecdl: 0.1193 0.1360 0.038 1.136 5.4 64.9 14.5 894 n/a 9_nqh: 0.1193 0.1360 0.038 1.136 5.4 64.9 14.5 894 n/a 9_sol: 0.1191 0.1349 0.038 1.136 5.4 64.9 14.5 902 n/a 9_weight: 0.1191 0.1349 0.038 1.136 5.4 64.9 14.5 902 n/a 9_xyzrec: 0.1195 0.1354 0.038 1.121 5.4 64.9 14.5 902 n/a 9_adp: 0.1196 0.1355 0.038 1.121 5.4 64.7 14.5 902 n/a 9_regHadp: 0.1196 0.1355 0.038 1.121 5.4 64.7 14.5 902 n/a 9_occ: 0.1195 0.1359 0.038 1.121 5.4 64.7 14.5 902 n/a 10_bss: 0.1194 0.1358 0.038 1.121 5.4 64.7 14.5 902 n/a 10_settarget: 0.1194 0.1358 0.038 1.121 5.4 64.7 14.5 902 n/a 10_updatecdl: 0.1194 0.1358 0.038 1.121 5.4 64.7 14.5 902 n/a 10_setrh: 0.1194 0.1358 0.038 1.121 5.4 64.7 14.5 902 n/a 10_nqh: 0.1195 0.1361 0.038 1.121 5.4 64.7 14.5 902 n/a 10_sol: 0.1194 0.1361 0.038 1.121 5.4 64.7 14.6 908 n/a 10_weight: 0.1194 0.1361 0.038 1.121 5.4 64.7 14.6 908 n/a 10_xyzrec: 0.1200 0.1369 0.039 1.187 5.4 64.7 14.6 908 n/a 10_adp: 0.1198 0.1369 0.039 1.187 5.4 63.9 14.6 908 n/a 10_regHadp: 0.1198 0.1369 0.039 1.187 5.4 63.9 14.6 908 n/a 10_occ: 0.1197 0.1370 0.039 1.187 5.4 63.9 14.6 908 n/a end: 0.1196 0.1369 0.039 1.187 5.4 63.9 14.6 908 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9707243_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9707243_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.4400 Refinement macro-cycles (run) : 12116.1000 Write final files (write_after_run_outputs) : 164.1900 Total : 12286.7300 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:57 PST -0800 (1736736117.10 s) Start R-work = 0.1804, R-free = 0.1942 Final R-work = 0.1196, R-free = 0.1369 =============================================================================== Job complete usr+sys time: 12570.54 seconds wall clock time: 210 minutes 29.04 seconds (12629.04 seconds total)